A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/project/lbarreiro/USERS/austin/slamseq/data/fastp_reports/project/lbarreiro/USERS/austin/slamseq/logs/hisat-3n/qc
General Statistics
| Sample Name | % Aligned | % Duplication | % > Q30 | Mb Q30 bases | Reads After Filtering | GC content | % PF | % Adapter | Mean R1 Length | Mean R2 Length |
|---|---|---|---|---|---|---|---|---|---|---|
| LB-HT-28s-HT-10_S10 | 47.7% | 94.1% | 64392.3Mb | 436.1M | 49.7% | 97.7% | 4.6% | 158.0bp | 158.0bp | |
| LB-HT-28s-HT-16_S16 | 37.5% | 93.7% | 59116.6Mb | 404.1M | 51.2% | 97.4% | 7.7% | 158.0bp | 158.0bp | |
| LB-HT-28s-HT-17_S17 | 50.0% | 0.0% | 68.2% | 0.0Mb | 0.0M | 57.7% | 14.7% | 0.0% | 158.0bp | 158.0bp |
| LB-HT-28s-HT-18_S18 | 82.3% | 39.3% | 93.8% | 56778.4Mb | 386.7M | 50.0% | 97.5% | 6.2% | 158.0bp | 158.0bp |
HISAT2
Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Please note that single mate alignment counts are halved to tally with pair counts properly.
fastp
1.0.1
All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560
Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.Filtered Reads
Filtering statistics of sampled reads.
Insert Sizes
Insert size estimation of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
GC Content
Average GC content over each base of all reads.
N content
Average N content over each base of all reads.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| fastp | 1.0.1 |